[BiO BB] SEQRES and ATOM record mismatch

Goel, Manisha MAG at Stowers-Institute.org
Thu Dec 9 11:03:47 EST 2004

Dear James,
Thank you so much for the generous offer.
That would have been really helpful, except that I already have the
alignments done according to the SEQRES record sequences, and this
pulling seqs out of the ATOMS would mean that I would have to repeat
that step.
So at present I am looking for any shortcut method to just transform the
residue id's from SEQRES to ATOMS record.
But In case that does not work too well (for many yet unforseen reasons,
I guess) Can I still come back for help later ?
Best Regards,

-----Original Message-----
From: bio_bulletin_board-bounces at bioinformatics.org
[mailto:bio_bulletin_board-bounces at bioinformatics.org] On Behalf Of
James Stroud
Sent: Wednesday, December 08, 2004 4:42 PM
To: The general forum at Bioinformatics.Org
Subject: Re: [BiO BB] SEQRES and ATOM record mismatch

Will a tool that pulls sequence from the ATOM records help?

If so, I have written one that does this. It can do it programatically
automatically for a large number of sequences). I can send it to you if
like. It is part a python API. I am still developing it, so there is no 
documentation, but I can write the two or three lines of code required
to use 
it for this purpose.


On Wednesday 08 December 2004 01:10 pm, Goel, Manisha wrote:
> Dear All,
> I have been using protein sequences of proteins with known structures 
> (PDB databse) derived from the SEQRES records. But now that I need to 
> run either DSSP or STRIDE on them.. I cannot map the secondary 
> structure back to the sequence alignments because the SEQRES and ATOMS

> records do not agree on the residue number id. So a residue numbered 
> as 278 in SEQRES record is listed as 268 in the ATOMS record, messing 
> up my alignments (I was using this numbering to map the secondary 
> structure on to the sequence) I have come across quite a bit of 
> discussion in some mailing lists about the need & proposed methods of 
> modification of the PDB files, so that they can be made consistent.
> BUT ..
> Meanwhile can somebody suggest a method or resource .. which could
> either fix this dicrepency or maybe a round about way of taking care
> this.
> I guess with people working with stuctural/sequence mapping so often,
> some such fix would have definetly been devised by somebody.
> I just want to be able to modify the residue numbers in the ATOMS 
> record to match the SEQRES records or something to that effect. CIF 
> does not work because it does not segregate by chain numbers/id.
> Thanks for any input,
> -MAnisha

James Stroud, Ph.D.
UCLA-DOE Institute for Genomics and Proteomics
611 Charles E. Young Dr. S.
MBI 205, UCLA 951570
Los Angeles CA 90095-1570
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